Starting phenix.real_space_refine on Wed Aug 5 11:58:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjh_39342/08_2026/8yjh_39342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjh_39342/08_2026/8yjh_39342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjh_39342/08_2026/8yjh_39342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjh_39342/08_2026/8yjh_39342.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjh_39342/08_2026/8yjh_39342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjh_39342/08_2026/8yjh_39342.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 55 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 63 5.16 5 C 5965 2.51 5 N 1631 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9735 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2769 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 1.90, per 1000 atoms: 0.20 Number of scatterers: 9735 At special positions: 0 Unit cell: (106.24, 95.45, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 53 15.00 O 2023 8.00 N 1631 7.00 C 5965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 261.0 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 28.9% alpha, 25.4% beta 14 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.262A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.975A pdb=" N LEU B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 222 " --> pdb=" O THR B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.729A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 209 through 217 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.528A pdb=" N LEU C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 222 " --> pdb=" O THR C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'A' and resid 8 through 19 removed outlier: 4.365A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.744A pdb=" N ALA D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.711A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.561A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.767A pdb=" N SER D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.967A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 242 through 252 removed outlier: 3.650A pdb=" N VAL D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.744A pdb=" N ILE D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.503A pdb=" N PHE D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.836A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.713A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 47 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 238 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.563A pdb=" N VAL B 111 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 207 removed outlier: 4.523A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 167 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 88 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.863A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 251 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 238 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 136 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 198 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 127 removed outlier: 3.753A pdb=" N GLY D 348 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY C 127 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 346 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 208 removed outlier: 4.863A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 99 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 59 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71 removed outlier: 3.620A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 249 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 136 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 198 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21 removed outlier: 3.571A pdb=" N ARG D 19 " --> pdb=" O GLU D 206 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 204 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.799A pdb=" N LYS D 30 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA D 176 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ALA D 32 " --> pdb=" O ALA D 176 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2732 1.34 - 1.46: 2131 1.46 - 1.58: 4920 1.58 - 1.70: 102 1.70 - 1.82: 102 Bond restraints: 9987 Sorted by residual: bond pdb=" C3' DT J 8 " pdb=" C2' DT J 8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT J 10 " pdb=" C2' DT J 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT E 5 " pdb=" C2' DT E 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.71e+00 bond pdb=" C THR C 219 " pdb=" N PRO C 220 " ideal model delta sigma weight residual 1.335 1.362 -0.027 9.40e-03 1.13e+04 8.22e+00 bond pdb=" C1' DT E 25 " pdb=" N1 DT E 25 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.04e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 13066 2.27 - 4.53: 505 4.53 - 6.80: 78 6.80 - 9.06: 37 9.06 - 11.33: 10 Bond angle restraints: 13696 Sorted by residual: angle pdb=" CA GLU B 132 " pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " ideal model delta sigma weight residual 114.10 123.74 -9.64 2.00e+00 2.50e-01 2.32e+01 angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.16e+01 angle pdb=" O GLN A 131 " pdb=" C GLN A 131 " pdb=" N GLU A 132 " ideal model delta sigma weight residual 122.39 128.16 -5.77 1.29e+00 6.01e-01 2.00e+01 angle pdb=" C LYS B 254 " pdb=" N ILE B 255 " pdb=" CA ILE B 255 " ideal model delta sigma weight residual 121.70 129.65 -7.95 1.80e+00 3.09e-01 1.95e+01 angle pdb=" N3 DT H 3 " pdb=" C4 DT H 3 " pdb=" O4 DT H 3 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 13691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5024 17.60 - 35.19: 688 35.19 - 52.79: 280 52.79 - 70.38: 48 70.38 - 87.98: 13 Dihedral angle restraints: 6053 sinusoidal: 2807 harmonic: 3246 Sorted by residual: dihedral pdb=" CA MET C 199 " pdb=" C MET C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ASN B 71 " pdb=" C ASN B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE D 33 " pdb=" C ILE D 33 " pdb=" N ASP D 34 " pdb=" CA ASP D 34 " ideal model delta harmonic sigma weight residual 180.00 157.56 22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 6050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1132 0.054 - 0.108: 339 0.108 - 0.162: 80 0.162 - 0.216: 21 0.216 - 0.270: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA THR A 219 " pdb=" N THR A 219 " pdb=" C THR A 219 " pdb=" CB THR A 219 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL A 236 " pdb=" CA VAL A 236 " pdb=" CG1 VAL A 236 " pdb=" CG2 VAL A 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE D 44 " pdb=" CA ILE D 44 " pdb=" CG1 ILE D 44 " pdb=" CG2 ILE D 44 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1575 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 274 " -0.020 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP D 274 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP D 274 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 274 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 274 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 274 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 274 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 132 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C GLU A 132 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 132 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 133 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.236 9.50e-02 1.11e+02 1.07e-01 8.83e+00 pdb=" NE ARG A 5 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.001 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1834 2.79 - 3.31: 8023 3.31 - 3.84: 17211 3.84 - 4.37: 19369 4.37 - 4.90: 32874 Nonbonded interactions: 79311 Sorted by model distance: nonbonded pdb=" OE2 GLU A 192 " pdb=" OG SER A 223 " model vdw 2.256 3.040 nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.306 3.040 nonbonded pdb=" O THR C 216 " pdb=" OG1 THR C 219 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR C 211 " pdb=" O SER D 25 " model vdw 2.357 3.040 nonbonded pdb=" O ASN B 71 " pdb=" OG SER B 74 " model vdw 2.366 3.040 ... (remaining 79306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 254) selection = (chain 'C' and resid 1 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.610 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9988 Z= 0.339 Angle : 1.074 11.331 13698 Z= 0.636 Chirality : 0.058 0.270 1578 Planarity : 0.007 0.107 1583 Dihedral : 18.972 87.975 3944 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.21), residues: 1107 helix: -2.74 (0.20), residues: 307 sheet: -2.02 (0.27), residues: 331 loop : -2.36 (0.23), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 5 TYR 0.022 0.003 TYR B 133 PHE 0.037 0.003 PHE D 27 TRP 0.062 0.004 TRP D 274 HIS 0.007 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.34 ( 9987) covalent geometry : angle 1.07355 / 0.64 (13696) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 2.40126 / 1.33 ( 2) hydrogen bonds : bond 0.19943 / 13.08 ( 431) hydrogen bonds : angle 9.94013 / 6.93 ( 1208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.213 Fit side-chains REVERT: B 184 GLN cc_start: 0.6862 (tm-30) cc_final: 0.6491 (tm-30) REVERT: C 201 GLU cc_start: 0.7192 (pt0) cc_final: 0.6920 (pt0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0688 time to fit residues: 17.4825 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.144416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113250 restraints weight = 14661.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115958 restraints weight = 9791.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117799 restraints weight = 7351.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119205 restraints weight = 6032.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120012 restraints weight = 5210.739| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9988 Z= 0.185 Angle : 0.654 6.087 13698 Z= 0.354 Chirality : 0.047 0.197 1578 Planarity : 0.005 0.044 1583 Dihedral : 19.268 78.285 1802 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.93 % Allowed : 8.36 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.22), residues: 1107 helix: -0.96 (0.27), residues: 304 sheet: -1.94 (0.26), residues: 327 loop : -2.07 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 5 TYR 0.014 0.002 TYR C 211 PHE 0.013 0.001 PHE D 126 TRP 0.029 0.002 TRP D 274 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 9987) covalent geometry : angle 0.65418 / 0.35 (13696) SS BOND : bond 0.00275 / 0.14 ( 1) SS BOND : angle 0.48067 / 0.27 ( 2) hydrogen bonds : bond 0.04665 / 3.00 ( 431) hydrogen bonds : angle 7.13494 / 4.96 ( 1208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.317 Fit side-chains REVERT: B 177 ASN cc_start: 0.7745 (t0) cc_final: 0.7414 (t0) REVERT: B 199 MET cc_start: 0.7598 (tmm) cc_final: 0.7025 (tpp) REVERT: C 201 GLU cc_start: 0.7246 (pt0) cc_final: 0.6990 (pt0) REVERT: D 127 THR cc_start: 0.8850 (p) cc_final: 0.8541 (t) REVERT: D 202 LEU cc_start: 0.7459 (mm) cc_final: 0.7146 (mt) outliers start: 9 outliers final: 6 residues processed: 145 average time/residue: 0.0718 time to fit residues: 16.5290 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 0.0980 chunk 101 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115322 restraints weight = 14623.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118811 restraints weight = 10861.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119377 restraints weight = 7409.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119676 restraints weight = 6581.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120497 restraints weight = 5997.373| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9988 Z= 0.117 Angle : 0.563 6.529 13698 Z= 0.307 Chirality : 0.044 0.201 1578 Planarity : 0.004 0.038 1583 Dihedral : 19.281 73.235 1802 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.14 % Allowed : 11.56 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.23), residues: 1107 helix: -0.25 (0.28), residues: 306 sheet: -1.82 (0.26), residues: 327 loop : -1.82 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 5 TYR 0.016 0.001 TYR A 250 PHE 0.009 0.001 PHE D 126 TRP 0.041 0.002 TRP D 274 HIS 0.008 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 9987) covalent geometry : angle 0.56301 / 0.31 (13696) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.66332 / 0.36 ( 2) hydrogen bonds : bond 0.03790 / 2.45 ( 431) hydrogen bonds : angle 6.55352 / 4.55 ( 1208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.252 Fit side-chains REVERT: B 177 ASN cc_start: 0.7788 (t0) cc_final: 0.7468 (t0) REVERT: B 199 MET cc_start: 0.7429 (tmm) cc_final: 0.7152 (tpp) REVERT: C 1 MET cc_start: 0.7442 (tpp) cc_final: 0.7219 (tpp) REVERT: C 121 LEU cc_start: 0.8473 (tp) cc_final: 0.8003 (tt) REVERT: A 135 CYS cc_start: 0.8115 (p) cc_final: 0.7835 (p) REVERT: D 40 TYR cc_start: 0.7749 (m-10) cc_final: 0.7348 (m-10) REVERT: D 202 LEU cc_start: 0.7459 (mm) cc_final: 0.7209 (mt) outliers start: 11 outliers final: 5 residues processed: 138 average time/residue: 0.0687 time to fit residues: 15.0581 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 HIS ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.142917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111488 restraints weight = 14680.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114252 restraints weight = 9750.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116215 restraints weight = 7314.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.117607 restraints weight = 5953.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118402 restraints weight = 5140.264| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9988 Z= 0.160 Angle : 0.575 7.397 13698 Z= 0.310 Chirality : 0.045 0.190 1578 Planarity : 0.003 0.034 1583 Dihedral : 19.155 75.151 1802 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.14 % Allowed : 14.14 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.23), residues: 1107 helix: 0.22 (0.29), residues: 306 sheet: -1.84 (0.26), residues: 331 loop : -1.75 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.013 0.002 TYR A 250 PHE 0.014 0.001 PHE D 126 TRP 0.026 0.002 TRP D 274 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 9987) covalent geometry : angle 0.57505 / 0.31 (13696) SS BOND : bond 0.00221 / 0.12 ( 1) SS BOND : angle 0.71164 / 0.38 ( 2) hydrogen bonds : bond 0.03604 / 2.35 ( 431) hydrogen bonds : angle 6.20565 / 4.31 ( 1208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.290 Fit side-chains REVERT: B 177 ASN cc_start: 0.7795 (t0) cc_final: 0.7503 (t0) REVERT: C 1 MET cc_start: 0.7558 (tpp) cc_final: 0.7172 (tpp) REVERT: C 121 LEU cc_start: 0.8425 (tp) cc_final: 0.8006 (tt) REVERT: A 68 MET cc_start: 0.7967 (ptp) cc_final: 0.7730 (ptp) REVERT: A 135 CYS cc_start: 0.8109 (p) cc_final: 0.7840 (p) REVERT: D 127 THR cc_start: 0.8914 (p) cc_final: 0.8611 (t) REVERT: D 202 LEU cc_start: 0.7467 (mm) cc_final: 0.7251 (mt) REVERT: D 326 LYS cc_start: 0.8062 (pttm) cc_final: 0.7339 (mmtp) outliers start: 11 outliers final: 9 residues processed: 140 average time/residue: 0.0730 time to fit residues: 15.3089 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110592 restraints weight = 14582.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114199 restraints weight = 11010.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114739 restraints weight = 7465.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114973 restraints weight = 6698.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115870 restraints weight = 6074.371| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9988 Z= 0.153 Angle : 0.581 9.913 13698 Z= 0.309 Chirality : 0.044 0.232 1578 Planarity : 0.003 0.033 1583 Dihedral : 19.082 74.794 1802 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.65 % Allowed : 14.65 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.24), residues: 1107 helix: 0.42 (0.29), residues: 309 sheet: -1.88 (0.26), residues: 311 loop : -1.54 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.015 0.002 TYR A 250 PHE 0.010 0.001 PHE D 126 TRP 0.026 0.002 TRP D 274 HIS 0.005 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 9987) covalent geometry : angle 0.58121 / 0.31 (13696) SS BOND : bond 0.00226 / 0.12 ( 1) SS BOND : angle 0.67893 / 0.36 ( 2) hydrogen bonds : bond 0.03424 / 2.21 ( 431) hydrogen bonds : angle 5.97887 / 4.13 ( 1208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.300 Fit side-chains REVERT: B 199 MET cc_start: 0.7366 (tpp) cc_final: 0.6741 (tpp) REVERT: C 1 MET cc_start: 0.7554 (tpp) cc_final: 0.7174 (tpp) REVERT: A 68 MET cc_start: 0.7958 (ptp) cc_final: 0.7617 (ptp) REVERT: A 135 CYS cc_start: 0.8157 (p) cc_final: 0.7873 (p) REVERT: D 127 THR cc_start: 0.8908 (p) cc_final: 0.8576 (t) REVERT: D 326 LYS cc_start: 0.8080 (pttm) cc_final: 0.7354 (mmtp) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 0.0780 time to fit residues: 15.5975 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 chunk 26 optimal weight: 0.7980 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.138395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106446 restraints weight = 14688.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109152 restraints weight = 9845.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111036 restraints weight = 7414.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112379 restraints weight = 6095.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113301 restraints weight = 5280.509| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9988 Z= 0.206 Angle : 0.625 9.573 13698 Z= 0.326 Chirality : 0.046 0.252 1578 Planarity : 0.003 0.032 1583 Dihedral : 19.008 74.300 1802 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.68 % Allowed : 15.58 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.24), residues: 1107 helix: 0.45 (0.29), residues: 309 sheet: -1.93 (0.26), residues: 309 loop : -1.44 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 211 TYR 0.016 0.002 TYR B 133 PHE 0.013 0.002 PHE D 126 TRP 0.024 0.002 TRP D 274 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 ( 9987) covalent geometry : angle 0.62536 / 0.33 (13696) SS BOND : bond 0.00220 / 0.12 ( 1) SS BOND : angle 1.01438 / 0.53 ( 2) hydrogen bonds : bond 0.03675 / 2.42 ( 431) hydrogen bonds : angle 5.91345 / 4.10 ( 1208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.389 Fit side-chains REVERT: B 36 ASN cc_start: 0.8443 (m-40) cc_final: 0.8230 (m-40) REVERT: B 177 ASN cc_start: 0.7812 (t0) cc_final: 0.7546 (t0) REVERT: B 199 MET cc_start: 0.7301 (tpp) cc_final: 0.6549 (tpp) REVERT: C 75 MET cc_start: 0.8818 (ttt) cc_final: 0.8515 (ttt) REVERT: A 135 CYS cc_start: 0.8213 (p) cc_final: 0.7975 (p) REVERT: D 326 LYS cc_start: 0.8229 (pttm) cc_final: 0.7531 (mmtp) outliers start: 26 outliers final: 16 residues processed: 145 average time/residue: 0.0733 time to fit residues: 16.0902 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107646 restraints weight = 14529.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110371 restraints weight = 9632.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112147 restraints weight = 7238.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113577 restraints weight = 5959.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114461 restraints weight = 5168.359| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9988 Z= 0.159 Angle : 0.598 10.178 13698 Z= 0.313 Chirality : 0.045 0.236 1578 Planarity : 0.003 0.033 1583 Dihedral : 18.952 74.253 1802 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.17 % Allowed : 16.31 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.24), residues: 1107 helix: 0.57 (0.29), residues: 309 sheet: -1.93 (0.26), residues: 309 loop : -1.40 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 129 TYR 0.017 0.002 TYR A 250 PHE 0.010 0.001 PHE D 126 TRP 0.023 0.002 TRP D 274 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 9987) covalent geometry : angle 0.59785 / 0.31 (13696) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 0.84906 / 0.45 ( 2) hydrogen bonds : bond 0.03397 / 2.22 ( 431) hydrogen bonds : angle 5.81682 / 4.02 ( 1208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.355 Fit side-chains REVERT: B 108 GLN cc_start: 0.7624 (mp10) cc_final: 0.7409 (mp10) REVERT: B 177 ASN cc_start: 0.7868 (t0) cc_final: 0.7596 (t0) REVERT: B 199 MET cc_start: 0.7238 (tpp) cc_final: 0.6443 (tpp) REVERT: A 135 CYS cc_start: 0.8176 (p) cc_final: 0.7969 (p) REVERT: D 127 THR cc_start: 0.8883 (p) cc_final: 0.8578 (t) REVERT: D 326 LYS cc_start: 0.8254 (pttm) cc_final: 0.7551 (mmtp) outliers start: 21 outliers final: 16 residues processed: 139 average time/residue: 0.0803 time to fit residues: 16.7932 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107870 restraints weight = 14505.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110559 restraints weight = 9581.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112273 restraints weight = 7210.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113774 restraints weight = 5953.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114607 restraints weight = 5148.469| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9988 Z= 0.156 Angle : 0.599 10.755 13698 Z= 0.311 Chirality : 0.045 0.232 1578 Planarity : 0.003 0.032 1583 Dihedral : 18.877 74.733 1802 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.06 % Allowed : 17.65 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.24), residues: 1107 helix: 0.69 (0.29), residues: 309 sheet: -1.91 (0.26), residues: 319 loop : -1.32 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 339 TYR 0.015 0.002 TYR A 250 PHE 0.011 0.002 PHE D 126 TRP 0.025 0.002 TRP D 274 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 9987) covalent geometry : angle 0.59905 / 0.31 (13696) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 0.95779 / 0.51 ( 2) hydrogen bonds : bond 0.03358 / 2.18 ( 431) hydrogen bonds : angle 5.73776 / 3.97 ( 1208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.367 Fit side-chains REVERT: B 108 GLN cc_start: 0.7624 (mp10) cc_final: 0.7356 (mp10) REVERT: B 177 ASN cc_start: 0.7884 (t0) cc_final: 0.7619 (t0) REVERT: B 199 MET cc_start: 0.7196 (tpp) cc_final: 0.6390 (tpp) REVERT: A 135 CYS cc_start: 0.8159 (p) cc_final: 0.7941 (p) REVERT: D 44 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8462 (mp) REVERT: D 127 THR cc_start: 0.8919 (p) cc_final: 0.8613 (t) REVERT: D 326 LYS cc_start: 0.8255 (pttm) cc_final: 0.7625 (mmtp) outliers start: 20 outliers final: 14 residues processed: 136 average time/residue: 0.0808 time to fit residues: 16.5154 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 0.0050 chunk 101 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105972 restraints weight = 14528.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108640 restraints weight = 9642.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110556 restraints weight = 7257.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111805 restraints weight = 5934.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112792 restraints weight = 5172.100| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9988 Z= 0.191 Angle : 0.624 10.698 13698 Z= 0.324 Chirality : 0.045 0.214 1578 Planarity : 0.003 0.032 1583 Dihedral : 18.834 73.574 1802 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.17 % Allowed : 17.96 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.25), residues: 1107 helix: 0.70 (0.29), residues: 308 sheet: -1.95 (0.26), residues: 319 loop : -1.29 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 64 TYR 0.016 0.002 TYR A 250 PHE 0.013 0.002 PHE D 126 TRP 0.022 0.002 TRP D 274 HIS 0.007 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 9987) covalent geometry : angle 0.62428 / 0.32 (13696) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 1.39709 / 0.75 ( 2) hydrogen bonds : bond 0.03559 / 2.33 ( 431) hydrogen bonds : angle 5.76054 / 3.98 ( 1208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.263 Fit side-chains REVERT: B 108 GLN cc_start: 0.7733 (mp10) cc_final: 0.7404 (mp10) REVERT: B 177 ASN cc_start: 0.7900 (t0) cc_final: 0.7615 (t0) REVERT: B 199 MET cc_start: 0.7221 (tpp) cc_final: 0.6287 (tpp) REVERT: D 44 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8508 (mp) REVERT: D 127 THR cc_start: 0.8938 (p) cc_final: 0.8625 (t) REVERT: D 326 LYS cc_start: 0.8417 (pttm) cc_final: 0.7689 (mmtp) outliers start: 21 outliers final: 17 residues processed: 139 average time/residue: 0.0604 time to fit residues: 12.7173 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117411 restraints weight = 14725.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119848 restraints weight = 10494.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.121016 restraints weight = 7906.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121327 restraints weight = 7241.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121545 restraints weight = 6447.036| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9988 Z= 0.155 Angle : 0.602 10.324 13698 Z= 0.314 Chirality : 0.044 0.197 1578 Planarity : 0.003 0.030 1583 Dihedral : 18.766 73.369 1802 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.86 % Allowed : 18.78 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.25), residues: 1107 helix: 0.81 (0.29), residues: 305 sheet: -1.97 (0.26), residues: 309 loop : -1.28 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 5 TYR 0.016 0.002 TYR A 250 PHE 0.013 0.002 PHE D 316 TRP 0.021 0.002 TRP D 274 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 9987) covalent geometry : angle 0.60231 / 0.31 (13696) SS BOND : bond 0.00057 / 0.03 ( 1) SS BOND : angle 1.13619 / 0.62 ( 2) hydrogen bonds : bond 0.03303 / 2.13 ( 431) hydrogen bonds : angle 5.70000 / 3.94 ( 1208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.260 Fit side-chains REVERT: B 108 GLN cc_start: 0.7722 (mp10) cc_final: 0.7396 (mp10) REVERT: B 177 ASN cc_start: 0.7900 (t0) cc_final: 0.7651 (t0) REVERT: B 199 MET cc_start: 0.7202 (tpp) cc_final: 0.6251 (tpp) REVERT: B 233 VAL cc_start: 0.7748 (t) cc_final: 0.7513 (t) REVERT: C 91 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6184 (mtm110) REVERT: D 44 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8505 (mp) REVERT: D 127 THR cc_start: 0.8920 (p) cc_final: 0.8620 (t) REVERT: D 326 LYS cc_start: 0.8374 (pttm) cc_final: 0.7678 (mmtp) outliers start: 18 outliers final: 15 residues processed: 135 average time/residue: 0.0654 time to fit residues: 13.2216 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120134 restraints weight = 14691.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122187 restraints weight = 10385.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123628 restraints weight = 8366.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123874 restraints weight = 7167.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124098 restraints weight = 6705.478| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9988 Z= 0.123 Angle : 0.597 13.074 13698 Z= 0.310 Chirality : 0.044 0.201 1578 Planarity : 0.003 0.033 1583 Dihedral : 18.687 74.307 1802 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.65 % Allowed : 19.71 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.25), residues: 1107 helix: 0.87 (0.29), residues: 308 sheet: -1.91 (0.26), residues: 319 loop : -1.19 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.014 0.002 TYR A 250 PHE 0.011 0.001 PHE B 215 TRP 0.020 0.001 TRP D 274 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9987) covalent geometry : angle 0.59684 / 0.31 (13696) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.88628 / 0.48 ( 2) hydrogen bonds : bond 0.03104 / 2.01 ( 431) hydrogen bonds : angle 5.55444 / 3.84 ( 1208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1420.88 seconds wall clock time: 25 minutes 21.22 seconds (1521.22 seconds total)